Data Pre-release QC

Purpose: Create a set of QC requirements for pre-release files which should pass before hand off between BIXU Engineering team to the OpenPedCan team.

Usage

To run this from the command line, use:

Rscript -e "rmarkdown::render('data-pre-release-qc.Rmd', clean = TRUE)"

This assumes you are in the modules directory of the repository, OpenPedCan-analysis/analyses/data-pre-release-qc.

Setup

• Load libraries

# R analysis packages
suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(data.table))

# Magrittr pipe
`%>%` <- dplyr::`%>%`

• Set up directories.

# directories for input and output files
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
data_dir <- file.path(root_dir, "data")
analyses_dir <- file.path(root_dir, "analyses")
results_dir <- file.path(analyses_dir, "data-pre-release-qc", "results")

# Create results folder if it doesn't exist
if (!dir.exists(results_dir)) {
  dir.create(results_dir)
}

Functions

• Output table function

missing_biospecimen_table <- function(hist_df, missing_ids, output_file) {
  missing_ids_df <- hist_df %>% 
    dplyr::filter(Kids_First_Biospecimen_ID %in% missing_ids) %>% 
    dplyr::select(Kids_First_Biospecimen_ID, 
                  Kids_First_Participant_ID,
                  experimental_strategy,
                  sample_type,
                  RNA_library, 
                  cohort)
  readr::write_tsv(missing_ids_df, file.path(results_dir, output_file))
  return(missing_ids_df)
}

Histologies file

• Load histologies file

# read file
hist_df <- readr::read_tsv(file.path(data_dir, "histologies-base.tsv"), 
                           guess_max = 10000,
                           col_types = cols(.default = col_guess()))

Check OpenPedCan RNA-Seq biospecimen IDs

• Expected counts matrix (gene-counts-rsem-expected_count-collapsed.rds)

# get OpenPedCan rnaseq biospecimen ids
hist_ids <- hist_df %>%
  filter(experimental_strategy == "RNA-Seq", cohort != "TCGA") %>%
  dplyr::pull(Kids_First_Biospecimen_ID)

# check that all OpenPedCan RNA-Seq biospecimen IDs are in the expected count expression matrix
biospecimen_ids <- readr::read_rds(file.path(data_dir,
                                        "gene-counts-rsem-expected_count-collapsed.rds")) %>%
  colnames()
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-gene-counts-rsem-expected_count-collapsed.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("RNA-Seq biospecimen in histolgies missing in gene-counts-rsem-expected_count-collapsed.rds = ", length(missing_ids)))

[1] "RNA-Seq biospecimen in histolgies missing in gene-counts-rsem-expected_count-collapsed.rds =  17382"

if (length(missing_hist_ids) > 0) {
  output_file <- "gene-counts-rsem-expected_count-collapsed-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}
print(paste("RNA-Seq biospecimen in gene-counts-rsem-expected_count-collapsed.rds missing in histolgies = ", length(missing_hist_ids)))

[1] "RNA-Seq biospecimen in gene-counts-rsem-expected_count-collapsed.rds missing in histolgies =  0"

• TPM matrix (gene-expression-rsem-tpm-collapsed.rds)

# check that all OpenPedCan RNA-Seq biospecimen IDs are in the tpm expression matrix
biospecimen_ids <- readr::read_rds(file.path(data_dir,
                                        "gene-expression-rsem-tpm-collapsed.rds")) %>%
  colnames()
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-gene-expression-rsem-tpm-collapsed.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("RNA-Seq biospecimen in histolgies missing in gene-expression-rsem-tpm-collapsed.rds = ", length(missing_ids)))

[1] "RNA-Seq biospecimen in histolgies missing in gene-expression-rsem-tpm-collapsed.rds =  17382"

if (length(missing_hist_ids) > 0) {
  output_file <- "gene-expression-rsem-tpm-collapsed-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}
print(paste("RNA-Seq biospecimen in gene-expression-rsem-tpm-collapsed.rds missing in histolgies = ", length(missing_hist_ids)))

[1] "RNA-Seq biospecimen in gene-expression-rsem-tpm-collapsed.rds missing in histolgies =  0"

• Isoform TPM matrix (rna-isoform-expression-rsem-tpm.rds)

# exclude GTEx biospecimen when checking isoform matrix
isoform_hist_df <-  hist_df %>%
  filter(experimental_strategy == "RNA-Seq", !cohort %in% c("TCGA","GTEx"))
  
isoform_hist_ids <- isoform_hist_df %>% dplyr::pull(Kids_First_Biospecimen_ID)

# check that all OpenPedCan RNA-Seq biospecimen IDs are in the tpm expression matrix
biospecimen_ids <- readr::read_rds(file.path(data_dir,
                                        "rna-isoform-expression-rsem-tpm.rds")) %>%
  dplyr::select(-c("transcript_id", "gene_symbol")) %>%
  colnames()
missing_ids <- setdiff(isoform_hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, isoform_hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-rna-isoform-expression-rsem-tpm.tsv"
  missing_ids_df <- missing_biospecimen_table(isoform_hist_df, missing_ids, output_file)
  missing_ids_df
}
print(paste("RNA-Seq biospecimen in histolgies missing in rna-isoform-expression-rsem-tpm.rds = ", length(missing_ids)))

[1] "RNA-Seq biospecimen in histolgies missing in rna-isoform-expression-rsem-tpm.rds =  0"

if (length(missing_hist_ids) > 0) {
  output_file <- "rna-isoform-expression-rsem-tpm-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("RNA-Seq biospecimen in rna-isoform-expression-rsem-tpm.rds missing in histolgies = ", length(missing_hist_ids)))

[1] "RNA-Seq biospecimen in rna-isoform-expression-rsem-tpm.rds missing in histolgies =  14"

Check TCGA RNA-Seq biospecimen IDs

• TPM matrix (tcga-gene-expression-rsem-tpm-collapsed.rds)

# get tcga rnaseq biospecimen ids
hist_ids <- hist_df %>%
  filter(experimental_strategy == "RNA-Seq", cohort == "TCGA") %>%
  dplyr::pull(Kids_First_Biospecimen_ID)

# check that all TCGA RNA-Seq biospecimen IDs are in the tpm expression matrix
biospecimen_ids <- readr::read_rds(file.path(data_dir,
                                        "tcga-gene-expression-rsem-tpm-collapsed.rds")) %>%
  colnames()
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-tcga-gene-expression-rsem-tpm-collapsed.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("RNA-Seq biospecimen in histolgies missing in tcga-gene-expression-rsem-tpm-collapsed.rds = ", length(missing_ids)))

[1] "RNA-Seq biospecimen in histolgies missing in tcga-gene-expression-rsem-tpm-collapsed.rds =  3"

if (length(missing_hist_ids) > 0) {
  output_file <- "tcga-gene-expression-rsem-tpm-collapsed-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("RNA-Seq biospecimen in tcga-gene-expression-rsem-tpm-collapsed.rds missing in histolgies = ", length(missing_hist_ids)))

[1] "RNA-Seq biospecimen in tcga-gene-expression-rsem-tpm-collapsed.rds missing in histolgies =  712"

Check gene symbols in gene expression matrices

• RNA-Seq expression matrices

# OPC counts matrix
opc_counts <-
  tibble::tibble(OPC_COUNTS =
    readr::read_rds(file.path(data_dir, "gene-counts-rsem-expected_count-collapsed.rds")) %>%
      rownames() %>% unique()) %>%
  dplyr::mutate(gene_symbol = OPC_COUNTS)

# OPC tpm matrix
opc_tpm <-
  tibble::tibble(OPC_TPM =
    readr::read_rds(file.path(data_dir, "gene-expression-rsem-tpm-collapsed.rds")) %>%
      rownames() %>% unique()) %>%
  dplyr::mutate(gene_symbol = OPC_TPM)

# # TCGA counts matrix
# tcga-counts <-
#   tibble::tibble(TCGA_COUNTS =
#     readr::read_rds(file.path(data_dir, "tcga-gene-counts-rsem-expected_count-collapsed.rds")) %>%
#       rownames() %>% unique()) %>%
#   dplyr::mutate(gene_symbol = TCGA_COUNTS)

# TCGA tpm matrix
tcga_tpm <-
  tibble::tibble(TCGA_TPM =
    readr::read_rds(file.path(data_dir, "tcga-gene-expression-rsem-tpm-collapsed.rds")) %>%
      rownames() %>% unique()) %>%
  dplyr::mutate(gene_symbol = TCGA_TPM)

# merge and list differences
gene_symbol_diffs <- opc_counts %>%
  dplyr::full_join(opc_tpm, by = "gene_symbol") %>%
  dplyr::full_join(tcga_tpm, by = "gene_symbol") %>%
  dplyr::select(-gene_symbol) %>%
  dplyr::filter(is.na(OPC_COUNTS) | is.na(OPC_TPM) | is.na(TCGA_TPM)) %>%
  dplyr::distinct()

# check any differences in gene symbols among gene matrices
if (length(rownames(gene_symbol_diffs)) > 0) {
  output_file <- "genes_not_in_all_gene_expression_matrices.tsv"
  gene_symbol_diffs %>% readr::write_tsv(file.path(results_dir, output_file))
  gene_symbol_diffs
}

print(paste("Genes not matching all expression matrices =", length(rownames(gene_symbol_diffs))))

[1] "Genes not matching all expression matrices = 27245"

Check methylation matrices biospecimen IDs

• Beta-values matrix (methyl-beta-values.rds)

# get beta-values methylation biospecimen ids
hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy == "Methylation") %>%
  dplyr::pull(Kids_First_Biospecimen_ID)

# check that all methylation biospecimen IDs are in the beta-values methylation matrix
biospecimen_ids <- readr::read_rds(file.path(data_dir, "methyl-beta-values.rds")) %>%
  dplyr::select(-Probe_ID) %>%
  colnames()
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-methyl-beta-values.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("Methylation biospecimen in histolgies missing in methyl-beta-values.rds = ", length(missing_ids)))

[1] "Methylation biospecimen in histolgies missing in methyl-beta-values.rds =  717"

if (length(missing_hist_ids) > 0) {
  output_file <- "methyl-beta-values-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("Methylation biospecimen in methyl-beta-values.rds missing in histolgies = ", length(missing_hist_ids)))

[1] "Methylation biospecimen in methyl-beta-values.rds missing in histolgies =  717"

• M-values matrix (methyl-m-values.rds)

# check that all methylation biospecimen IDs are in the m-values methylation matrix
biospecimen_ids <- readr::read_rds(file.path(data_dir, "methyl-m-values.rds")) %>%
  dplyr::select(-Probe_ID) %>%
  colnames()
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-methyl-m-values.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("Methylation biospecimen in histolgies missing in methyl-m-values.rds = ", length(missing_ids)))

[1] "Methylation biospecimen in histolgies missing in methyl-m-values.rds =  717"

if (length(missing_hist_ids) > 0) {
  output_file <- "methyl-m-values-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("Methylation biospecimen in methyl-m-values.rds missing in histolgies = ", length(missing_hist_ids)))

[1] "Methylation biospecimen in methyl-m-values.rds missing in histolgies =  717"

• CN-values matrix (methyl-m-values.rds)

# check that all methylation biospecimen IDs are in the m-values methylation matrix
biospecimen_ids <- readr::read_rds(file.path(data_dir, "methyl-cn-values.rds")) %>%
  dplyr::select(-Probe_ID) %>%
  colnames()
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-methyl-cn-values.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("Methylation biospecimen in histolgies missing in methyl-cn-values.rds = ", length(missing_ids)))

[1] "Methylation biospecimen in histolgies missing in methyl-cn-values.rds =  717"

if (length(missing_hist_ids) > 0) {
  output_file <- "methyl-cn-values-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("Methylation biospecimen in methyl-cn-values.rds missing in histolgies = ", length(missing_hist_ids)))

[1] "Methylation biospecimen in methyl-cn-values.rds missing in histolgies =  717"

Check methylation matrices probe IDs

• Methylation matrices

# beta-values matrix
beta_values <-
  tibble::tibble(beta_values =
    readr::read_rds(file.path(data_dir, "methyl-beta-values.rds")) %>%
      dplyr::pull(Probe_ID) %>% unique()) %>%
  dplyr::mutate(probe_id = beta_values)

# m-values matrix
m_values <-
  tibble::tibble(m_values =
    readr::read_rds(file.path(data_dir, "methyl-m-values.rds")) %>%
      dplyr::pull(Probe_ID) %>% unique()) %>%
  dplyr::mutate(probe_id = m_values)

# cn-values matrix
cn_values <-
  tibble::tibble(cn_values =
    readr::read_rds(file.path(data_dir, "methyl-cn-values.rds")) %>%
      dplyr::pull(Probe_ID) %>% unique()) %>%
  dplyr::mutate(probe_id = cn_values)

# merge and list differences
probe_id_diffs <- beta_values %>%
  dplyr::full_join(m_values, by = "probe_id") %>%
  dplyr::full_join(cn_values, by = "probe_id") %>%
  dplyr::select(-probe_id) %>%
  dplyr::filter(is.na(beta_values) | is.na(m_values) | is.na(cn_values)) %>%
  dplyr::distinct()

# check any differences in probe IDs among methyl matrices
if (length(rownames(probe_id_diffs)) > 0) {
  output_file <- "probes_not_in_all_methyl_matrices.tsv"
  gene_symbol_diffs %>% readr::write_tsv(file.path(results_dir, output_file))
  gene_symbol_diffs
}
print(paste("Probes not matching all methylation matrices =", length(rownames(probe_id_diffs))))

[1] "Probes not matching all methylation matrices = 0"

Check DNA SNV, CNV and SV biospecimen IDs

• CNVkit seg file (cnv-cnvkit.seg.gz)

# check that all biospecimen IDs are in the file
biospecimen_ids <- readr::read_tsv(file.path(data_dir, "cnv-cnvkit.seg.gz")) %>%
  dplyr::pull(ID) %>%
  unique()

Rows: 4297481 Columns: 7
-- Column specification -----------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (2): ID, chrom
dbl (5): loc.start, loc.end, num.mark, seg.mean, copy.num

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.

hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy %in% c("WGS", "WXS"),
                !is.na(pathology_diagnosis)) %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-cnv-cnvkit.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("DNA biospecimen in histolgies missing in cnv-cnvkit.seg.gz = ", length(missing_ids)))

[1] "DNA biospecimen in histolgies missing in cnv-cnvkit.seg.gz =  293"

if (length(missing_hist_ids) > 0) {
  output_file <- "cnv-cnvkit.seg-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("DNA biospecimen in cnv-cnvkit.seg.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "DNA biospecimen in cnv-cnvkit.seg.gz missing in histolgies =  500"

• Control-FREEC file (cnv-controlfreec.tsv.gz)

# check that all  biospecimen IDs are in the file
biospecimen_ids <- readr::read_tsv(file.path(data_dir, "cnv-controlfreec.tsv.gz")) %>%
  dplyr::pull(Kids_First_Biospecimen_ID) %>%
  unique()

Rows: 3123454 Columns: 11
-- Column specification -----------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (4): Kids_First_Biospecimen_ID, chr, status, genotype
dbl (7): start, end, copy number, uncertainty, WilcoxonRankSumTestPvalue, Ko...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.

hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy %in% c("WGS", "WXS"), 
                !is.na(pathology_diagnosis)) %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-cnv-controlfreec.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("DNA biospecimen in histolgies missing in cnv-controlfreec.tsv.gz = ", length(missing_ids)))

[1] "DNA biospecimen in histolgies missing in cnv-controlfreec.tsv.gz =  293"

if (length(missing_hist_ids) > 0) {
  output_file <- "cnv-controlfreec-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("DNA biospecimen in cnv-controlfreec.tsv.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "DNA biospecimen in cnv-controlfreec.tsv.gz missing in histolgies =  500"

• GATK seg file (cnv-gatk.seg.gz)

# check that all biospecimen IDs are in the file
biospecimen_ids <- readr::read_tsv(file.path(data_dir, "cnv-gatk.seg.gz")) %>%
  dplyr::pull(BS_ID) %>%
  unique()

Rows: 1732889 Columns: 7
-- Column specification -----------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (3): BS_ID, CONTIG, CALL
dbl (4): START, END, NUM_POINTS_COPY_RATIO, MEAN_LOG2_COPY_RATIO

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.

hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy %in% c("WGS"), 
                !is.na(pathology_diagnosis)) %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-cnv-gatk.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("DNA biospecimen in histolgies missing in cnv-gatk.seg.gz = ", length(missing_ids)))

[1] "DNA biospecimen in histolgies missing in cnv-gatk.seg.gz =  280"

if (length(missing_hist_ids) > 0) {
  output_file <- "cnv-gatk-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("DNA biospecimen in cnv-gatk.seg.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "DNA biospecimen in cnv-gatk.seg.gz missing in histolgies =  105"

• SNV consensus MAF file (snv-consensus-plus-hotspots.maf.tsv.gz)

# check that all biospecimen IDs are in the file
snv_consensus_maf <- data.table::fread(file.path(data_dir,
                                                 "snv-consensus-plus-hotspots.maf.tsv.gz"),
                                       data.table = FALSE)
biospecimen_ids <- snv_consensus_maf %>% 
  dplyr::pull(Tumor_Sample_Barcode) %>%
  unique()
hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy %in% c("WGS", "WXS", "Targeted Sequencing"),
                !is.na(pathology_diagnosis),
                cohort != "DGD") %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-snv-consensus-plus-hotspots.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("DNA biospecimen in histolgies missing in snv-consensus-plus-hotspots.maf.tsv.gz = ", length(missing_ids)))

[1] "DNA biospecimen in histolgies missing in snv-consensus-plus-hotspots.maf.tsv.gz =  356"

if (length(missing_hist_ids) > 0) {
  output_file <- "snv-consensus-plus-hotspots-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}
print(paste("DNA biospecimen in snv-consensus-plus-hotspots.maf.tsv.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "DNA biospecimen in snv-consensus-plus-hotspots.maf.tsv.gz missing in histolgies =  0"

• SNV DGD MAF file (snv-dgd.maf.tsv.gz)

# check that all biospecimen IDs are in the file
snv_dgd_maf <- data.table::fread(file.path(data_dir, "snv-dgd.maf.tsv.gz"), 
                                 data.table = FALSE)
biospecimen_ids <- snv_dgd_maf %>% 
  dplyr::pull(Tumor_Sample_Barcode) %>%
  unique()
hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy == "Targeted Sequencing",
                is.na(RNA_library),
                !is.na(pathology_diagnosis), 
                cohort == "DGD") %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-snv-dgd.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}
print(paste("DNA biospecimen in histolgies missing in snv-dgd.maf.tsv.gz = ", length(missing_ids)))

[1] "DNA biospecimen in histolgies missing in snv-dgd.maf.tsv.gz =  0"

if (length(missing_hist_ids) > 0) {
  output_file <- "snv-dgd-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}
print(paste("DNA biospecimen in snv-dgd.maf.tsv.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "DNA biospecimen in snv-dgd.maf.tsv.gz missing in histolgies =  0"

• Check column class differences between DGD and consensus SNV MAF

# consensus maf column class
snv_consensus_maf <- snv_consensus_maf %>% 
  dplyr::summarise_all(class) %>% 
  tidyr::pivot_longer(colnames(.), names_to = "variable", values_to = "consensus")

# dgd maf column class
snv_dgd_maf <- snv_dgd_maf %>% 
  dplyr::summarise_all(class) %>% 
  tidyr::pivot_longer(colnames(.), names_to = "variable", values_to = "DGD")

# diffs between DGD and consensus
maff_class_diffs <- snv_consensus_maf %>% 
  dplyr::full_join(snv_dgd_maf, by = "variable") %>% 
  filter(is.na(consensus) | is.na(DGD) | consensus != DGD)
maff_class_diffs

# write to file
output_file <- "snv-column-class-diffs-consensus-vs-dgd.tsv"
maff_class_diffs %>% readr::write_tsv(file.path(results_dir, output_file))

• SV Manta file (sv-manta.tsv.gz)

# check that all biospecimen IDs are in the file
biospecimen_ids <- data.table::fread(file.path(data_dir,
                                               "sv-manta.tsv.gz"),
                                     data.table = FALSE) %>%
  dplyr::pull(Kids.First.Biospecimen.ID.Tumor) %>%
  unique()
hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy %in% c("WGS", "WXS"),
                !is.na(pathology_diagnosis)) %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-sv-manta"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("DNA biospecimen in histolgies missing in sv-manta.tsv.gz = ", length(missing_ids)))

[1] "DNA biospecimen in histolgies missing in sv-manta.tsv.gz =  1631"

if (length(missing_hist_ids) > 0) {
  output_file <- "sv-manta-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("DNA biospecimen in sv-manta.tsv.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "DNA biospecimen in sv-manta.tsv.gz missing in histolgies =  20"

• Biospecimen to bed file mapping (biospecimen_id_to_bed_map.tsv)

# check that all biospecimen IDs have associated with a bed file
biospecimen_ids <- readr::read_tsv(file.path(data_dir, "biospecimen_id_to_bed_map.tsv")) %>%
  dplyr::pull(Kids_First_Biospecimen_ID) %>%
  unique()

Rows: 5654 Columns: 2
-- Column specification -----------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (2): Kids_First_Biospecimen_ID, bed_to_use

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.

hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy %in% c("WGS", "WXS", "Targeted Sequencing"),
                !is.na(pathology_diagnosis),
                cohort != "DGD") %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-biospecimen_id_to_bed_map.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("DNA biospecimen in histolgies missing in biospecimen_id_to_bed_map.tsv = ", length(missing_ids)))

[1] "DNA biospecimen in histolgies missing in biospecimen_id_to_bed_map.tsv =  18"

if (length(missing_hist_ids) > 0) {
  output_file <- "biospecimen_id_to_bed_map-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("DNA biospecimen in biospecimen_id_to_bed_map.tsv missing in histolgies = ", length(missing_hist_ids)))

[1] "DNA biospecimen in biospecimen_id_to_bed_map.tsv missing in histolgies =  1062"

Check RNA splice events and fusions biospecimen IDs

• rMATS file (splice-events-rmats.tsv.gz)

# check that all biospecimen IDs are in the file
biospecimen_ids <- data.table::fread(file.path(data_dir,
                                               "splice-events-rmats.tsv.gz"),
                                     data.table = FALSE) %>%
  dplyr::pull(sample_id) %>%
  unique()

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

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Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Avoidable 22.415 seconds. This file is very unusual: it ends abruptly without a final newline, and also its size is a multiple of 4096 bytes. Please properly end the last row with a newline using for example 'echo >> file' to avoid this  time to copy.

Warning in data.table::fread(file.path(data_dir, "splice-events-
rmats.tsv.gz"), : Discarded single-line footer: <<A5SS BS_J70GK8SM NA
ENSG00000135678.12 CPM chr12>>

hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy == "RNA-Seq",
               !is.na(pathology_diagnosis),
               !cohort %in% c("TCGA", "GTEx")) %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_ids <- setdiff(hist_ids, biospecimen_ids)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_ids) > 0) {
  output_file <- "histologies-samples-missing-in-splice-events-rmats.tsv"
  missing_ids_df <- missing_biospecimen_table(hist_df, missing_ids, output_file)
  missing_ids_df
}

print(paste("RNA biospecimen in histolgies missing in splice-events-rmats.tsv.gz = ", length(missing_ids)))

[1] "RNA biospecimen in histolgies missing in splice-events-rmats.tsv.gz =  1379"

if (length(missing_hist_ids) > 0) {
  output_file <- "splice-events-rmats-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}

print(paste("RNA biospecimen in splice-events-rmats.tsv.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "RNA biospecimen in splice-events-rmats.tsv.gz missing in histolgies =  14"

• AnnoFuse file (fusion-annoFuse.tsv.gz)

# check that all biospecimen IDs are in the file
biospecimen_ids <- readr::read_tsv(file.path(data_dir, "fusion-annoFuse.tsv.gz")) %>%
  dplyr::pull(Sample) %>%
  unique()

Rows: 232319 Columns: 22
-- Column specification -----------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (18): Sample, FusionName, LeftBreakpoint, RightBreakpoint, Caller, Fusio...
dbl  (3): JunctionReadCount, SpanningFragCount, SpanningDelta
lgl  (1): reciprocal_exists

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.

hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy == "RNA-Seq", 
                !cohort %in% c("DGD", "TCGA", "GTEx")) %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_hist_ids) > 0) {
  output_file <- "fusion-annoFuse-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}
print(paste("RNA biospecimen in fusion-annoFuse.tsv.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "RNA biospecimen in fusion-annoFuse.tsv.gz missing in histolgies =  0"

• Arriba fusion file (fusion-arriba.tsv.gz)

# check that all biospecimen IDs are in the file
biospecimen_ids <- readr::read_tsv(file.path(data_dir, "fusion-arriba.tsv.gz")) %>%
  dplyr::pull(tumor_id) %>%
  unique()

Rows: 282056 Columns: 33
-- Column specification -----------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (28): gene1, gene2, strand1.gene.fusion., strand2.gene.fusion., breakpoi...
dbl  (5): split_reads1, split_reads2, discordant_mates, coverage1, coverage2

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.

hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy == "RNA-Seq", 
                !cohort %in% c("DGD", "TCGA", "GTEx")) %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_hist_ids) > 0) {
  output_file <- "fusion-annoFuse-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}
print(paste("RNA biospecimen in fusion-arriba.tsv.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "RNA biospecimen in fusion-arriba.tsv.gz missing in histolgies =  0"

• STAR-Fusion file (fusion-starfusion.tsv.gz)

# check that all biospecimen IDs are in the file
biospecimen_ids <- readr::read_tsv(file.path(data_dir, "fusion-starfusion.tsv.gz")) %>%
  dplyr::pull(tumor_id) %>%
  unique()

Rows: 12694 Columns: 28
-- Column specification -----------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (21): FusionName, SpliceType, LeftGene, LeftBreakpoint, RightGene, Right...
dbl  (7): JunctionReadCount, SpanningFragCount, est_J, est_S, FFPM, LeftBrea...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.

hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy == "RNA-Seq", 
                !cohort %in% c("DGD", "TCGA", "GTEx")) %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_hist_ids) > 0) {
  output_file <- "fusion-starfusion-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}
print(paste("RNA biospecimen in fusion-starfusion.tsv.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "RNA biospecimen in fusion-starfusion.tsv.gz missing in histolgies =  0"

• Fusion DGD file (fusion-dgd.tsv.gz)

# check that all biospecimen IDs are in the file
biospecimen_ids <- readr::read_tsv(file.path(data_dir, "fusion-dgd.tsv.gz")) %>%
  dplyr::pull(Sample) %>%
  unique()

Rows: 278 Columns: 17
-- Column specification -----------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (9): Sample, FusionName, Fusion_Type, Gene1A, Gene1B, annots, Gene1A_ann...
dbl (2): JunctionReadCount, SpanningFragCount
lgl (6): Gene2A, Gene2B, LeftBreakpoint, RightBreakpoint, Gene2A_anno, Gene2...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.

hist_ids <- hist_df %>%
  dplyr::filter(experimental_strategy == "Targeted Sequencing", 
                !is.na(RNA_library),
                cohort == "DGD") %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
missing_hist_ids <- setdiff(biospecimen_ids, hist_ids)
if (length(missing_hist_ids) > 0) {
  output_file <- "fusion-dgd-samples-missing-in-histologies.tsv"
  missing_hist_ids_df <- tibble::tibble(Kids_First_Biospecimen_ID = missing_hist_ids)
  missing_hist_ids_df %>% readr::write_tsv(file.path(results_dir, output_file))
  missing_hist_ids_df
}
print(paste("RNA biospecimen in fusion-dgd.tsv.gz missing in histolgies = ", length(missing_hist_ids)))

[1] "RNA biospecimen in fusion-dgd.tsv.gz missing in histolgies =  0"

Session Info

sessionInfo() 

R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS/LAPACK: /home/ubuntu/volume/miniconda3/lib/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=C                 LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] data.table_1.14.2 forcats_0.5.2     stringr_1.4.1     dplyr_1.0.10     
 [5] purrr_0.3.4       readr_2.1.2       tidyr_1.2.0       tibble_3.1.8     
 [9] ggplot2_3.3.6     tidyverse_1.3.2  

loaded via a namespace (and not attached):
 [1] lubridate_1.8.0     assertthat_0.2.1    rprojroot_2.0.3    
 [4] digest_0.6.29       utf8_1.2.2          R6_2.5.1           
 [7] cellranger_1.1.0    backports_1.4.1     reprex_2.0.2       
[10] evaluate_0.16       httr_1.4.4          pillar_1.8.1       
[13] rlang_1.0.5         googlesheets4_1.0.1 readxl_1.4.1       
[16] jquerylib_0.1.4     R.oo_1.25.0         R.utils_2.12.0     
[19] rmarkdown_2.16      googledrive_2.0.0   bit_4.0.4          
[22] munsell_0.5.0       broom_1.0.1         compiler_4.1.3     
[25] modelr_0.1.9        xfun_0.32           pkgconfig_2.0.3    
[28] htmltools_0.5.3     tidyselect_1.1.2    fansi_1.0.3        
[31] crayon_1.5.1        tzdb_0.3.0          dbplyr_2.2.1       
[34] withr_2.5.0         R.methodsS3_1.8.2   grid_4.1.3         
[37] jsonlite_1.8.0      gtable_0.3.1        lifecycle_1.0.1    
[40] DBI_1.1.3           magrittr_2.0.3      scales_1.2.1       
[43] cli_3.3.0           stringi_1.7.8       vroom_1.5.7        
[46] cachem_1.0.6        fs_1.5.2            xml2_1.3.3         
[49] bslib_0.4.0         ellipsis_0.3.2      generics_0.1.3     
[52] vctrs_0.4.1         tools_4.1.3         bit64_4.0.5        
[55] glue_1.6.2          hms_1.1.2           parallel_4.1.3     
[58] fastmap_1.1.0       yaml_2.3.5          colorspace_2.0-3   
[61] gargle_1.2.1        rvest_1.0.3         knitr_1.40         
[64] haven_2.5.1         sass_0.4.2